Difference between revisions of "GGBN Data Standard v1"

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'''2016-08-26: This page is currently under construction.'''
 
'''2016-08-26: This page is currently under construction.'''
  
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This page describes the GGBN Data Standard version 1 (v1), released on xxth September 2016. In addition to this wiki page the document is available as pdf, rdf and SKOS. ###ADD_LINKS###
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This page describes the GGBN Data Standard version 1 (v1), released on xxth September 2016. In addition to this wiki page the document is available as pdf. ###ADD_LINKS###
  
 
'''Citation:'''  
 
'''Citation:'''  
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Droege et al. (in press): The Global Genome Biodiversity Network (GGBN) Standard Specification. DATABASE. doi: 10.1093/database/baw125
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Droege et al. (2016): The Global Genome Biodiversity Network (GGBN) Standard Specification. DATABASE. doi: 10.1093/database/baw125
  
 
'''Note:'''
 
'''Note:'''
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Ongoing discussions and updates of the GGBN Data Standard will be documented at http://terms.tdwg.org/GGBN_Data_Standard  
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Ongoing discussions and updates of the GGBN Data Standard will be documented at http://terms.tdwg.org/GGBN_Data_Standard
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'''The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution!''' Implementations are available for both ABCD and [http://rs.gbif.org/extension/ggbn/ DarwinCore-Archive]. For ABCD two implementations have been made. One for single species samples [http://data.ggbn.org/schemas/ggbn/terms/ABCDGGBN.html ABCDGGBN] and one for environmental samples [http://data.ggbn.org/schemas/ggbn/Enviro/ABCDGGBN_Enviro.html ABCDGGBN-Enviro]. Please check out the [http://terms.tdwg.org/GGBN_Data_Standard TDWG wiki] for updates.
  
 
A new stable version of the standard will be released earliest at the end of 2019.
 
A new stable version of the standard will be released earliest at the end of 2019.
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</div>
 
</div>
  
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The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary standards, such as [[http://rs.tdwg.org/dwc/terms/ | DwC]], [[http://www.bgbm.org/TDWG/CODATA/Schema/ABCD_2.06/HTML/ABCD_2.06.html | ABCD]] or [[http://gensc.org/mixs/ | MIxS]]. Potentially, the standard can be used not only for non-human genomic samples but also human samples. It builds upon existing standards commonly used within the communities extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard incorporates all molecular terms of [[http://gensc.org/mixs/ | MIxS]], and can also handle [[http://www.isber.org/?page=SPREC | SPREC]] and large parts of [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169291/ | BRISQ]]. It has been developed as a cross-domain effort lead by the Global Genome Biodiversity Network together with colleagues from [[http://rs.tdwg.org/dwc/terms/ | DwC]], [[http://www.bgbm.org/TDWG/CODATA/Schema/ABCD_2.06/HTML/ABCD_2.06.html | ABCD]], [[http://gensc.org/mixs/ | MIxS]], [[http://www.gbif.org | GBIF]], [[http://www.esbb.org | ESBB]] and others over the last years.
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The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary standards, such as [http://rs.tdwg.org/dwc/terms/ DwC], [http://www.bgbm.org/TDWG/CODATA/Schema/ABCD_2.06/HTML/ABCD_2.06.html ABCD] or [http://gensc.org/mixs/ MIxS]. Potentially, the standard can be used not only for non-human genomic samples but also human samples. It builds upon existing standards commonly used within the communities extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard incorporates all molecular terms of [http://gensc.org/mixs/ MIxS], and can also handle [http://www.isber.org/?page=SPREC SPREC] and large parts of [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169291/ BRISQ]. It has been developed as a cross-domain effort lead by the Global Genome Biodiversity Network together with colleagues from [http://rs.tdwg.org/dwc/terms/ DwC], [http://www.bgbm.org/TDWG/CODATA/Schema/ABCD_2.06/HTML/ABCD_2.06.html ABCD], [http://gensc.org/mixs/ MIxS], [http://www.gbif.org GBIF], [http://www.esbb.org ESBB] and others over the last years.
  
 
''<u>Contributors:</u> Gabi Droege, Katharine Barker, Walter G. Berendsohn, Sean Brady, Carol Butler, E. Margaret Casey, Jonathan Coddington, John Deck, David Fichtmüller, Birgit Gemeinholzer, Anton Güntsch, Jörg Holetschek, Tom Hollowell, Patricia Kelbert, Hans-Peter Klenk, Renzo Kottmann, Christopher Lewis, Chris Lyal, Jacqueline Mackenzie-Dodds, Christopher Meyer, Daniel Mulcahy, Éamonn Ó Tuama, Thomas Orrell, Gitte Petersen, Astrid Schories, Ole Seberg, Jamie Whitacre, Pelin Yilmaz, Holger Zetzsche, Yong Zhang, Xin Zhou, Erica Benson, Boyke Bunk, Enrique Arbeláez Cortés, Boyke Bunk, René Dekker, Markus Döring, Sonya Dyhrman, Paul Flemons, Elisabeth Haring, Thomas Knebelsberger, Ivayolo Kostadinov, Rita T. Lawlor, Jon Norenburg, Sara Y. Nussbeck, Michael Raupach, Thomas von Rintelen, Tim Robertson, Larissa Smirnova, Carola Söhngen, Sun Ying, Lee A. Weigt, John Wieczorek, Kenneth Wurdack, Elizabeth Zimmer.''  
 
''<u>Contributors:</u> Gabi Droege, Katharine Barker, Walter G. Berendsohn, Sean Brady, Carol Butler, E. Margaret Casey, Jonathan Coddington, John Deck, David Fichtmüller, Birgit Gemeinholzer, Anton Güntsch, Jörg Holetschek, Tom Hollowell, Patricia Kelbert, Hans-Peter Klenk, Renzo Kottmann, Christopher Lewis, Chris Lyal, Jacqueline Mackenzie-Dodds, Christopher Meyer, Daniel Mulcahy, Éamonn Ó Tuama, Thomas Orrell, Gitte Petersen, Astrid Schories, Ole Seberg, Jamie Whitacre, Pelin Yilmaz, Holger Zetzsche, Yong Zhang, Xin Zhou, Erica Benson, Boyke Bunk, Enrique Arbeláez Cortés, Boyke Bunk, René Dekker, Markus Döring, Sonya Dyhrman, Paul Flemons, Elisabeth Haring, Thomas Knebelsberger, Ivayolo Kostadinov, Rita T. Lawlor, Jon Norenburg, Sara Y. Nussbeck, Michael Raupach, Thomas von Rintelen, Tim Robertson, Larissa Smirnova, Carola Söhngen, Sun Ying, Lee A. Weigt, John Wieczorek, Kenneth Wurdack, Elizabeth Zimmer.''  

Revision as of 11:32, 30 September 2016

2016-08-26: This page is currently under construction.

This page describes the GGBN Data Standard version 1 (v1), released on xxth September 2016. In addition to this wiki page the document is available as pdf. ###ADD_LINKS###

Citation: Droege et al. (2016): The Global Genome Biodiversity Network (GGBN) Standard Specification. DATABASE. doi: 10.1093/database/baw125

Note: Ongoing discussions and updates of the GGBN Data Standard will be documented at http://terms.tdwg.org/GGBN_Data_Standard

The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution! Implementations are available for both ABCD and DarwinCore-Archive. For ABCD two implementations have been made. One for single species samples ABCDGGBN and one for environmental samples ABCDGGBN-Enviro. Please check out the TDWG wiki for updates.

A new stable version of the standard will be released earliest at the end of 2019.

The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary standards, such as DwC, ABCD or MIxS. Potentially, the standard can be used not only for non-human genomic samples but also human samples. It builds upon existing standards commonly used within the communities extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard incorporates all molecular terms of MIxS, and can also handle SPREC and large parts of BRISQ. It has been developed as a cross-domain effort lead by the Global Genome Biodiversity Network together with colleagues from DwC, ABCD, MIxS, GBIF, ESBB and others over the last years.

Contributors: Gabi Droege, Katharine Barker, Walter G. Berendsohn, Sean Brady, Carol Butler, E. Margaret Casey, Jonathan Coddington, John Deck, David Fichtmüller, Birgit Gemeinholzer, Anton Güntsch, Jörg Holetschek, Tom Hollowell, Patricia Kelbert, Hans-Peter Klenk, Renzo Kottmann, Christopher Lewis, Chris Lyal, Jacqueline Mackenzie-Dodds, Christopher Meyer, Daniel Mulcahy, Éamonn Ó Tuama, Thomas Orrell, Gitte Petersen, Astrid Schories, Ole Seberg, Jamie Whitacre, Pelin Yilmaz, Holger Zetzsche, Yong Zhang, Xin Zhou, Erica Benson, Boyke Bunk, Enrique Arbeláez Cortés, Boyke Bunk, René Dekker, Markus Döring, Sonya Dyhrman, Paul Flemons, Elisabeth Haring, Thomas Knebelsberger, Ivayolo Kostadinov, Rita T. Lawlor, Jon Norenburg, Sara Y. Nussbeck, Michael Raupach, Thomas von Rintelen, Tim Robertson, Larissa Smirnova, Carola Söhngen, Sun Ying, Lee A. Weigt, John Wieczorek, Kenneth Wurdack, Elizabeth Zimmer.


Namespace URI: http://data.ggbn.org/schemas/ggbn/terms/ with preferred namespace prefix “ggbn”.


GGBN Amplification Vocabulary

Index to GGBN Amplification Vocabulary

By label: Amplification Date • Amplification Method • Amplification Staff • Amplification Success • Amplification Success Details • BOLD Process ID • Barcode Sequence • Consensus Sequence • Consensus Sequence Chromatogram URI • Consensus Sequence Length • Genetic Accession Number • Genetic Accession URI • Guanin-Cytosine content • Haplotype • Marker • Marker Accordance • Marker Subfragment • Primer Name • Primer Name (Forward) • Primer Name (Reverse) • Primer Reference Citation • Primer Reference Citation (Forward) • Primer Reference Citation (Reverse) • Primer Reference Link • Primer Reference Link (Forward) • Primer Reference Link (Reverse) • Primer Sequence • Primer Sequence (Forward) • Primer Sequence (Reverse) • Purification Method (DNA or Amplification) • adapters • mixs:annot source • mixs:assembly • mixs:chimera check • mixs:finishing strategy • mixs:mid • mixs:seq quality check • mixs:sop

Concept definitions in GGBN Amplification Vocabulary

Concept Name: ggbn:amplificationDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/amplificationDate
Label Amplification Date
Definition Date when the amplification was carried out
  Required: No — Repeatable: Yes
Examples 2008-10-17, May 2007
Notes: freetext since mostly extact date is unknown
Concept Name: ggbn:amplificationMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/amplificationMethod
Label Amplification Method
Definition Method used for amplification/PCR.
  Required: No — Repeatable: Yes
Concept Name: ggbn:amplificationStaff
Normative URI http://data.ggbn.org/schemas/ggbn/terms/amplificationStaff
Label Amplification Staff
Definition Person or Institution who performed the amplification
  Required: No — Repeatable: Yes
Examples Jon Doe, NMNH
Concept Name: ggbn:amplificationSuccess
Normative URI http://data.ggbn.org/schemas/ggbn/terms/amplificationSuccess
Label Amplification Success
Definition true/false or yes/no whether the ampliciation was successful in general; highly recommended to report unsuccessful runs
  Required: No — Repeatable: Yes
Examples yes, no, true, false
Notes: should be used together with ggbn:amplificationSuccessDetails
Concept Name: ggbn:amplificationSuccessDetails
Normative URI http://data.ggbn.org/schemas/ggbn/terms/amplificationSuccessDetails
Label Amplification Success Details
Definition Details about the amplification, e.g. including why it has failed
  Required: No — Repeatable: Yes
Notes: should be used together with ggbn:amplificationSuccess
Concept Name: ggbn:barcodeSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/barcodeSequence
Label Barcode Sequence
Definition DNA Barcode sequence (part or 100% of the consensus sequence)
  Required: No — Repeatable: Yes
Concept Name: ggbn:BOLDProcessID
Normative URI http://data.ggbn.org/schemas/ggbn/terms/BOLDProcessID
Label BOLD Process ID
Definition Definite number or ID under which the DNA sequence is deposited in the BOLD database
  Required: No — Repeatable: Yes
Notes: often a BOLD record has also a genetic accession number at NCBI/EMBL/DDBJ in addition
Concept Name: ggbn:consensusSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/consensusSequence
Label Consensus Sequence
Definition Consensus sequence derived from all individual sequences
  Required: No — Repeatable: Yes
Concept Name: ggbn:consensusSequenceChromatogramFileURI
Normative URI http://data.ggbn.org/schemas/ggbn/terms/consensusSequenceChromatogramFileURI
Label Consensus Sequence Chromatogram URI
Definition Link to the chromatogram of the consensus sequence
  Required: No — Repeatable: Yes
Examples should start with http://
Concept Name: ggbn:consensusSequenceLength
Normative URI http://data.ggbn.org/schemas/ggbn/terms/consensusSequenceLength
Label Consensus Sequence Length
Definition Length of the consensus sequence (number of base pairs)
  Required: No — Repeatable: Yes
Examples 697, integer value
Concept Name: ggbn:GC-content
Normative URI http://data.ggbn.org/schemas/ggbn/terms/GC-content
Label Guanin-Cytosine content
Definition guanine-cytosine content in mol %
  Required: No — Repeatable: Yes
Concept Name: ggbn:geneticAccessionNumber
Normative URI http://data.ggbn.org/schemas/ggbn/terms/geneticAccessionNumber
Label Genetic Accession Number
Definition Definite number or ID under which the DNA sequence is deposited in a public database (GenBank/EMBL/DDBJ accession number)
  Required: No — Repeatable: Yes
Concept Name: ggbn:geneticAccessionURI
Normative URI http://data.ggbn.org/schemas/ggbn/terms/geneticAccessionURI
Label Genetic Accession URI
Definition URI of the related record in a public database (GenBank/DDBJ/EMBL record)
  Required: No — Repeatable: Yes
Examples should start with http://
Notes: this is to enable the provider to decide where to point to
Concept Name: ggbn:haplotype
Normative URI http://data.ggbn.org/schemas/ggbn/terms/haplotype
Label Haplotype
Definition Name of the haplotype
  Required: No — Repeatable: Yes
Examples H4, A23
Concept Name: ggbn:marker
Normative URI http://data.ggbn.org/schemas/ggbn/terms/marker
Label Marker
Definition Genetic locus/marker or DNA fragment amplified by PCR
  Required: No — Repeatable: Yes
Examples COI, rbcL
Concept Name: ggbn:markerAccordance
Normative URI http://data.ggbn.org/schemas/ggbn/terms/markerAccordance
Label Marker Accordance
Definition Result of comparison of two markers of two specimens or strains. Name or TAX-ID (NCBI) of compared specimens/strain and the relative identity percentage must be given
  Required: No — Repeatable: Yes
Concept Name: ggbn:markerSubfragment
Normative URI http://data.ggbn.org/schemas/ggbn/terms/markerSubfragment
Label Marker Subfragment
Definition Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes
  Required: No — Repeatable: Yes
Examples V6
Concept Name: ggbn:primerName
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerName
Label Primer Name
Definition Name of primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse
Concept Name: ggbn:primerNameForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerNameForward
Label Primer Name (Forward)
Definition Name of primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use #ggbn:primerName
Concept Name: ggbn:primerNameReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerNameReverse
Label Primer Name (Reverse)
Definition Name of reverse primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use #ggbn:primerName
Concept Name: ggbn:primerReferenceCitation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation
Label Primer Reference Citation
Definition Forst reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse
Concept Name: ggbn:primerReferenceCitationForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationForward
Label Primer Reference Citation (Forward)
Definition First reference of the forward rimer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation
Concept Name: ggbn:primerReferenceCitationReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationReverse
Label Primer Reference Citation (Reverse)
Definition First reference of the reverse primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink
Label Primer Reference Link
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse
ggbn:primerReferenceLinkForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkForward
Label Primer Reference Link (Forward)
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink
ggbn:primerReferenceLinkReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkReverse
Label Primer Reference Link (Reverse)
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink
Concept Name: ggbn:primerSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequence
Label Primer Sequence
Definition DNA sequence of the primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse
Concept Name: ggbn:primerSequenceForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward
Label Primer Sequence (Forward)
Definition DNA sequence of the forward primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence
Concept Name: ggbn:primerSequenceReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse
Label Primer Sequence (Reverse)
Definition DNA sequence of the reverse primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence
Concept Name: ggbn:purificationMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/purificationMethod
Label Purification Method (DNA or Amplification)
Definition Method or protocol used for secundary purification of already extracted genomic DNA or of PCR product
  Required: No — Repeatable: Yes
Examples QIAamp DNA Mini Kit
Notes: no controlled vocabulary; this element should be used both for DNA and Amplification product; repeatable only within GGBN Amplification Vocabulary
Concept Name: mixs:adapters
Normative URI http://gensc.org/ns/mixs/adapters
Label adapters
Definition Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
  Required: No — Repeatable: Yes
Concept Name: mixs:annot source
Normative URI http://gensc.org/ns/mixs/annot_source
Label annotation source
Definition For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
  Required: No — Repeatable: Yes
Concept Name: mixs:assembly
Normative URI http://gensc.org/ns/mixs/assembly
Label assembly
Definition How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler); estimated error rate associated with the finished sequences (e.g. error rate of 1 in 1000 bp); and the method of calculation
  Required: No — Repeatable: No
Concept Name: mixs:chimera check
Normative URI http://gensc.org/ns/mixs/chimera_check
Label chimera check
Definition A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point
  Required: No — Repeatable: No
Concept Name: mixs:finishing strategy
Normative URI http://gensc.org/ns/mixs/finishing_strategy
Label finishing strategy
Definition Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome
  Required: No — Repeatable: Yes
Concept Name: mixs:mid
Normative URI http://gensc.org/ns/mixs/mid
Label multiplex identifiers
Definition Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
  Required: No — Repeatable: Yes
Concept Name: mixs:seq quality check
Normative URI http://gensc.org/ns/mixs/seq_quality_check
Label sequence quality check
Definition Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA e.g. none or manually edited
  Required: No — Repeatable: Yes
Concept Name: mixs:sop
Normative URI http://gensc.org/ns/mixs/sop
Label relevant standard operating procedures
Definition Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
  Required: No — Repeatable: Yes

GGBN DNA Cloning Vocabulary

Index to GGBN DNA Cloning Vocabulary

By label: Clone Strain • Cloning Date • Cloning Method • Cloning Staff • Plasmid • Primer Name • Primer Name (Forward) • Primer Name (Reverse) • Primer Reference Citation • Primer Reference Citation (Forward) • Primer Reference Citation (Reverse) • Primer Reference Link • Primer Reference Link (Forward) • Primer Reference Link (Reverse) • Primer Sequence • Primer Sequence (Forward) • Primer Sequence (Reverse) • library construction method • library reads sequenced • library screening strategy • library size • library vector

By concept name: ggbn:cloneStrain • ggbn:cloningDate • ggbn:cloningMethod • ggbn:cloningStaff • ggbn:plasmid • ggbn:primerName • ggbn:primerNameForward • ggbn:primerNameReverse • ggbn:primerReferenceCitation • ggbn:primerReferenceLinkForward • ggbn:primerReferenceLinkReverse • ggbn:primerSequence • ggbn:primerSequenceForward • ggbn:primerSequenceReverse • mixs:lib const meth • mixs:lib reads seqd • mixs:lib screen • mixs:lib size • mixs:lib vector

Concept definitions in GGBN Cloning Vocabulary

Concept Name: ggbn:cloneStrain
Normative URI http://data.ggbn.org/schemas/ggbn/terms/cloneStrain
Label Clone Strain
Definition Name of the individual DNA clone
  Required: No — Repeatable: No
Concept Name: ggbn:cloningDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/cloningDate
Label Cloning Date
Definition Date when the DNA cloning was carried out
  Required: No — Repeatable: No
Examples 2014-05-18, May 2013
Concept Name: ggbn:cloningMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/cloningMethod
Label Cloning Method
Definition Method or protocol used for DNA cloning
  Required: No — Repeatable: No
Concept Name: ggbn:cloningStaff
Normative URI http://data.ggbn.org/schemas/ggbn/terms/cloningStaff
Label Cloning Staff
Definition Person or Institution who performed the cloning
  Required: No — Repeatable: No
Examples Jane Doe, NMNH
Concept Name: ggbn:plasmid
Normative URI http://data.ggbn.org/schemas/ggbn/terms/plasmid
Label Plasmid
Definition Name of Plasmid used for sequencing
  Required: No — Repeatable: No
Concept Name: ggbn:primerName
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerName
Label Primer Name
Definition Name of primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse
Concept Name: ggbn:primerNameForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerNameForward
Label Primer Name (Forward)
Definition Name of primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName
Concept Name: ggbn:primerNameReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerNameReverse
Label Primer Name (Reverse)
Definition Name of reverse primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName
Concept Name: ggbn:primerReferenceCitation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation
Label Primer Reference Citation
Definition Forst reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse
Concept Name: ggbn:primerReferenceCitationForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationForward
Label Primer Reference Citation (Forward)
Definition First reference of the forward rimer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation
Concept Name: ggbn:primerReferenceCitationReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitationReverse
Label Primer Reference Citation (Reverse)
Definition First reference of the reverse primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceCitation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink
Label Primer Reference Link
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse
ggbn:primerReferenceLinkForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkForward
Label Primer Reference Link (Forward)
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink
ggbn:primerReferenceLinkReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLinkReverse
Label Primer Reference Link (Reverse)
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerReferenceLink
Concept Name: ggbn:primerSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequence
Label Primer Sequence
Definition DNA sequence of the primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse
Concept Name: ggbn:primerSequenceForward
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward
Label Primer Sequence (Forward)
Definition DNA sequence of the forward primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence
Concept Name: ggbn:primerSequenceReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse
Label Primer Sequence (Reverse)
Definition DNA sequence of the reverse primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence
Concept Name: mixs:lib const meth
Normative URI http://gensc.org/ns/mixs/lib_const_meth
Label library construction method
Definition Library construction method used for clone libraries
  Required: No — Repeatable: No
Examples paired-end,single,vector
Concept Name: mixs:lib reads seqd
Normative URI http://gensc.org/ns/mixs/lib_reads_seqd
Label library reads sequenced
Definition Total number of clones sequenced from the library
  Required: No — Repeatable: No
Concept Name: mixs:lib screen
Normative URI http://gensc.org/ns/mixs/lib_screen
Label library screening strategy
Definition Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences
  Required: No — Repeatable: No
Examples enriched, screened, normalized
Concept Name: mixs:lib size
Normative URI http://gensc.org/ns/mixs/lib_size
Label library size
Definition Total number of clones in the library prepared for the project
  Required: No — Repeatable: No
Concept Name: mixs:lib vector
Normative URI http://gensc.org/ns/mixs/lib_vector
Label library vector
Definition Cloning vector type(s) used in construction of libraries
  Required: No — Repeatable: No

GGBN Gel Image Vocabulary

Index to GGBN Gel Image Vocabulary

By label: DNA Threshold • Gel Buffer • Gel Concentration • Gel Duration • Gel Ladder • Gel Remarks • Gel Stain • Gel Stain Concentration • Gel Voltage • Identifier • Percent above Threshold • Staining Method

By concept name: dcterms:identifier • ggbn:DNAThreshold • ggbn:gelBuffer • ggbn:gelConcentration • ggbn:gelDuration • ggbn:gelLadder • ggbn:gelRemarks • ggbn:gelStain • ggbn:gelStainConcentration • ggbn:gelVoltage • ggbn:percentAboveThreshold • ggbn:stainingMethod

Concept definitions in GGBN Gel Image Vocabulary

Concept Name: dcterms:identifier
Normative URI http://purl.org/dc/terms/identifier
Label Identifier
Definition An unambiguous reference to the resource within a given context.
  Required: No — Repeatable: No
Notes: Dublin Core: Recommended best practice is to identify the resource by means of a string conforming to a formal identification system. Audubon Core: An arbitrary code that is unique for the resource, with the resource being either a provider, collection, or media item. Using multiple identifiers implies that they have a same-as relationship, i.e. they all identify the same object (e. g. an object may have an http-URL, an lsid-URI, and a UUID-number).

Required for media collections, No for media resources (but preferred if available).

In context of GGBN used as gel image uri.

Concept Name: ggbn:DNAThreshold
Normative URI http://data.ggbn.org/schemas/ggbn/terms/DNAThreshold
Label DNA Threshold
Definition Fragment size of the ladder you choose as a standard to measure the percentage of your DNA size, at or above threshold fragment size from ladder
  Required: No — Repeatable: No
Examples 564; 2,027; 2,322; 4,361, 6,557; 9,416; 23,130. The hindIII ladder has fragment sizes (in base-pairs, bp): 564; 2,027; 2,322; 4,361, 6,557; 9,416; 23,130
Concept Name: ggbn:gelBuffer
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelBuffer
Label Gel Buffer
Definition Buffer used to make your gel and buffer in which you run the gel. The gel should be made with the same buffer in which it is run
  Required: No — Repeatable: No
Examples Tris-Boric Acid-EDTA
Concept Name: ggbn:gelConcentration
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelConcentration
Label Gel Concentration
Definition Concentration of your gel
  Required: No — Repeatable: No
Examples 0.7x, 1x, 1.5x
Concept Name: ggbn:gelDuration
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelDuration
Label Gel Duration
Definition Duration of Gel with unit
  Required: No — Repeatable: No
Concept Name: ggbn:gelLadder
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelLadder
Label Gel Ladder
Definition A Gel Ladder is a combination of various known-length fragments of DNA or RNA used to measure DNA or RNA fragments of unknown lengths.
  Required: No — Repeatable: No
Examples HindIII
Concept Name: ggbn:gelRemarks
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelRemarks
Label Gel Remarks
Definition General remarks on your gel.
  Required: No — Repeatable: No
Concept Name: ggbn:gelStain
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelStain
Label Gel Stain
Definition Type of gel stain used. Gel stain is a substance that binds to DNA and fluoresces under ultraviolet (UV) light.
  Required: No — Repeatable: No
Examples GelRed; SYBR-Safe; Ethidium Bromide (EtBr)
Concept Name: ggbn:gelStainConcentration
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelStainConcentration
Label Gel Stain Concentration
Definition Concentration of your gel stain
  Required: No — Repeatable: No
Examples 5ul of 10,000x into 50 ml of TBE buffer
Concept Name: ggbn:gelVoltage
Normative URI http://data.ggbn.org/schemas/ggbn/terms/gelVoltage
Label Gel Voltage
Definition Voltage of Gel (in V)
  Required: No — Repeatable: No
Concept Name: ggbn:percentAboveThreshold
Normative URI http://data.ggbn.org/schemas/ggbn/terms/percentAboveThreshold
Label Percent above Threshold
Definition Percent of your DNA at or above the size of the threshold
  Required: No — Repeatable: No
Examples 10%, 35%, 50%, 80%. Usually a protocol considers 50% of fragments ≥ 9KB to be high genomic quality
Concept Name: ggbn:stainingMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/stainingMethod
Label Staining Method
Definition Method used for staining gels, either precast-adding stain to your gel before casting; post stain-staining your gel after running; stain in loading buffer-adding the stain to the loading buffer
  Required: No — Repeatable: No
Examples Precast stain; Post stain; Stain in loading buffer

GGBN Loan Vocabulary

Index to GGBN Loan Vocabulary

By label: Blocked • Blocked Until • Disposition • Loan Conditions • Loan Date • Loan Destination,Loaned To • Loan Identifier,Loan Number • Received From

By concept name: dwc:disposition • ggbn:blocked • ggbn:blockedUntil • ggbn:loanConditions • ggbn:loanDate • ggbn:loanDestination • ggbn:loanIdentifier • ggbn:receivedFrom

Concept definitions in GGBN Loan Vocabulary

Concept Name: dwc:disposition
Normative URI http://rs.tdwg.org/dwc/terms/disposition
Label Disposition
Definition The current state of a specimen with respect to the collection identified in collectionCode or collectionID. Recommended best practice is to use a controlled vocabulary.
  Required: No — Repeatable: Yes
Examples "in collection", "missing", "voucher elsewhere", "duplicates elsewhere"
Notes: For discussion see http://code.google.com/p/darwincore/wiki/Occurrence

Remark by GGBN: "consumed" as another example

Concept Name: ggbn:blocked
Normative URI http://data.ggbn.org/schemas/ggbn/terms/blocked
Label Blocked
Definition Sample or specimen data can not be ordered/loaned in general, but are visible via portals.
  Required: No — Repeatable: Yes
Examples yes, no
Notes: Records/samples/specimens not to be published should be blocked on database level. If they are available via Darwin Core or ABCD, they are visible for everyone. This element is to be used for samples/specimens that cannot be loaned.
Concept Name: ggbn:blockedUntil
Normative URI http://data.ggbn.org/schemas/ggbn/terms/blockedUntil
Label Blocked Until
Definition Sample or specimen data can not be ordered/loaned until the given date, but are visible via portals
  Required: No — Repeatable: Yes
Examples 2016-03-31, format YYYY-MM-DD
Notes: in GGBN context the record is visible at the portal but blocked for ordering until the given date
Concept Name: ggbn:loanConditions
Normative URI http://data.ggbn.org/schemas/ggbn/terms/loanConditions
Label Loan Conditions
Definition Sample can be ordered under certain conditions, that are described here
  Required: No — Repeatable: Yes
Examples for non-commercial institutions only; only with permission of material supplier
Concept Name: ggbn:loanDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/loanDate
Label Loan Date
Definition Date when loan has been sent by the lender.
  Required: No — Repeatable: Yes
Notes: based on HISPID extension for ABCD
Concept Name: ggbn:loanDestination
Normative URI http://data.ggbn.org/schemas/ggbn/terms/loanDestination
Label Loan Destination,Loaned To
Definition Name of person and/or organization the unit was sent to. Person/Institution who received the material.
  Required: No — Repeatable: Yes
Examples Jane Doe, NMNH
Notes: based on HISPID extension for ABCD;

in this instance, “sent” is not equivalent to “shipped”. A shipment can be directed to a recipient who is not the actual intended responsible party; many organizations have shipping offices to handle packages.

Concept Name: ggbn:loanIdentifier
Normative URI http://data.ggbn.org/schemas/ggbn/terms/loanIdentifier
Label Loan Identifier,Loan Number
Definition The unique institutional loan number to uniquely identify a specimen on loan
  Required: No — Repeatable: Yes
Examples 2014/123
Notes: based on HISPID extension for ABCD
Concept Name: ggbn:receivedFrom
Normative URI http://data.ggbn.org/schemas/ggbn/terms/receivedFrom
Label Received From
Definition Name of person and/or organization the unit was received from. Person/Institution who authorized the loan of the material. From the perspective of the owner of the material, this type of loan is incoming.
  Required: No — Repeatable: Yes
Examples e.g. lender or recipient of a strain, sample, specimen etc.

GGBN Material Sample Vocabulary

Index to GGBN Material Sample Vocabulary

By label: Concentration (DNA) • DNA Melting Point • DNA-DNA Hybridization • High • Low • Material Sample Type • Medium • Method used for Determination of Concentration and Ratios of Absorbance (DNA) • Method used for Determination of Weight • Purification Method (DNA or Amplification) • Quality • Quality Check Date • Quality Remarks • Quality Vocabulary • Ratio of Absorbance 260/230 (DNA) • Ratio of Absorbance 260/280 (DNA) • Sample Designation • Unit of Concentration (DNA) • Unit of Volume • Unit of Weight • Volume • Weight • estimated Size • sample size

By concept name: ggbn:DNADNAHybridization • ggbn:DNAMeltingPoint • ggbn:concentration • ggbn:concentrationUnit • ggbn:materialSampleType • ggbn:methodDeterminationConcentrationAndRatios • ggbn:methodDeterminationWeight • ggbn:purificationMethod • ggbn:quality • ggbn:qualityCheckDate • ggbn:qualityRemarks • ggbn:ratioOfAbsorbance260 230 • ggbn:ratioOfAbsorbance260 280 • ggbn:sampleDesignation • ggbn:volume • ggbn:volumeUnit • ggbn:weight • ggbn:weightUnit • ggbnvoc:high • ggbnvoc:low • ggbnvoc:medium • ggbnvoc:quality vocabulary • mixs:estimated size • mixs:samp size

Concept definitions in GGBN Material Sample Vocabulary

Concept Name: ggbn:concentration
Normative URI http://data.ggbn.org/schemas/ggbn/terms/concentration
Label Concentration (DNA)
Definition Concentration of DNA (weight ng/volume µl)
  Required: No — Repeatable: No
Examples 67.5
Notes: in ABCD this element has stringUnit as attribute (example ng/µl)

in DarwinCore this element has to be used together with ggbn:concentrationUnit

Concept Name: ggbn:concentrationUnit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/concentrationUnit
Label Unit of Concentration (DNA)
Definition Unit used for concentration measurement (DNA)
  Required: No — Repeatable: No
Examples ng/µl
Notes: in DarwinCore this element has to be used together with ggbn:concentration

this element is not required in ABCD (see ggbn:concentration for details)

Concept Name: ggbn:DNADNAHybridization
Normative URI http://data.ggbn.org/schemas/ggbn/terms/DNADNAHybridization
Label DNA-DNA Hybridization
Definition Result of DNA-DNA hybridization, e.g. strain: measurement value percentage
  Required: No — Repeatable: No
Concept Name: ggbn:DNAMeltingPoint
Normative URI http://data.ggbn.org/schemas/ggbn/terms/DNAMeltingPoint
Label DNA Melting Point
Definition result of melting temperature (Tm) analysis, e.g. measurement value unit
  Required: No — Repeatable: No
Concept Name: ggbn:materialSampleType
Normative URI http://data.ggbn.org/schemas/ggbn/terms/materialSampleType
Label Material Sample Type
Definition Classification of kind of physical sample in addition to BasisOfRecord/RecordBasis and Preparation Type.
  Required: Yes — Repeatable: No
Examples tissue, culture strain, specimen, DNA, RNA, Protein, environmental sample
Notes: Please use preparationType for further specification such as 'leg','blood','gDNA','axenic culture'.

Equal to KindOfUnit in ABCD!

Concept Name: ggbn:methodDeterminationConcentrationAndRatios
Normative URI http://data.ggbn.org/schemas/ggbn/terms/methodDeterminationConcentrationAndRatios
Label Method used for Determination of Concentration and Ratios of Absorbance (DNA)
Definition Description of method used for concentration measurement (DNA)
  Required: No — Repeatable: No
Examples Nanodrop, Qubit
Concept Name: ggbn:methodDeterminationWeight
Normative URI http://data.ggbn.org/schemas/ggbn/terms/methodDeterminationWeight
Label Method used for Determination of Weight
Definition Description of method used for weight measurement
  Required: No — Repeatable: No
Examples Agarose gel, bioanalyzer, tape station
Notes: This element can be used for both DNA and tissue samples (or specimens)
Concept Name: ggbn:purificationMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/purificationMethod
Label Purification Method (DNA or Amplification)
Definition Method or protocol used for secundary purification of already extracted genomic DNA or of PCR product
  Required: No — Repeatable: Yes
Examples QIAamp DNA Mini Kit
Notes: no controlled vocabulary; this element should be used both for DNA and Amplification product; repeatable only within GGBN Amplification Vocabulary
Concept Name: ggbn:quality
Normative URI http://data.ggbn.org/schemas/ggbn/terms/quality
Label Quality
Definition Sample quality estimation based on parameters described at QualityRemarks
  Required: No — Repeatable: No
Examples high, medium, low
Notes: Predefined vocabulary! See: ggbn:quality vocabulary
Concept Name: ggbn:qualityCheckDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/qualityCheckDate
Label Quality Check Date
Definition Date of quality check (e.g. Nanodrop measurement (DNA))
  Required: No — Repeatable: No
Examples ISO format: 2013-01-27
Notes: this element can be used for DNA, tissues or specimens
Concept Name: ggbn:qualityRemarks
Normative URI http://data.ggbn.org/schemas/ggbn/terms/qualityRemarks
Label Quality Remarks
Definition Description of methods and parameters defining low, medium or high quality of a sample
  Required: No — Repeatable: No
Notes: to be used together with ggbn:quality
Concept Name: ggbn:ratioOfAbsorbance260 230
Normative URI http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_230
Label Ratio of Absorbance 260/230 (DNA)
Definition Ratio of absorbance at 260 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only)
  Required: No — Repeatable: No
Examples 1.89
Concept Name: ggbn:ratioOfAbsorbance260 280
Normative URI http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_280
Label Ratio of Absorbance 260/280 (DNA)
Definition Ratio of absorbance at 280 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only)
  Required: No — Repeatable: No
Examples 1.8
Notes: no controlled vocabulary
Concept Name: ggbn:sampleDesignation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sampleDesignation
Label Sample Designation
Definition Additional lab or project numbers used for the DNA or tissue sample.
  Required: No — Repeatable: No
Examples CAM123;CrCro456
Notes: In case of multiple numbers please separate them with ";"
Concept Name: ggbn:volume
Normative URI http://data.ggbn.org/schemas/ggbn/terms/volume
Label Volume
Definition Volume of sample
  Required: No — Repeatable: No
Examples 30, 150
Notes: this element can be used for DNA or tissue samples

in ABCD this element has stringUnit as attribute (example µl, ml)

in DarwinCore this element has to be used together with ggbn:volumeUnit

Concept Name: ggbn:volumeUnit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/volumeUnit
Label Unit of Volume
Definition Unit used for volume measurement
  Required: No — Repeatable: No
Examples µl, ml
Notes: in DarwinCore this element has to be used together with ggbn:volume

this element is not required in ABCD (see ggbn:volume for details)

Concept Name: ggbn:weight
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weight
Label Weight
Definition Weight of sample
  Required: No — Repeatable: No
Examples 10
Notes: this element can be used for DNA or tissue samples

in ABCD this element has stringUnit as attribute (example ng, mg, g)

in DarwinCore this element has to be used together with ggbn:weightUnit

Concept Name: ggbn:weightUnit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weightUnit
Label Unit of Weight
Definition Unit used for weight measurement
  Required: No — Repeatable: No
Examples ng, mg, g
Notes: in DarwinCore this element has to be used together with ggbn:weight

this element is not required in ABCD (see ggbn:weight for details)

Concept Name: ggbnvoc:high
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weightUnit
Label High
Definition A value for the ggbnvoc:quality_vocabulary
  Required: No — Repeatable: No
Concept Name: ggbnvoc:low
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weightUnit
Label Low
Definition A value for the ggbnvoc:quality_vocabulary
  Required: No — Repeatable: No
Concept Name: ggbnvoc:medium
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weightUnit
Label Medium
Definition A value for the ggbnvoc:quality_vocabulary
  Required: No — Repeatable: No
Concept Name: ggbnvoc:quality vocabulary
Normative URI http://data.ggbn.org/schemas/ggbn/terms/weightUnit
Label Quality Vocabulary
Definition Vocabulary of ggbn:quality term
  Required: No — Repeatable: No
Examples ggbnvoc:high, ggbnvoc:medium, ggbnvoc:low
Notes: Methods and parameters defining low, medium or high quality of a sample are described with ggbn:qualityRemarks
Concept Name: mixs:estimated size
Normative URI http://gensc.org/ns/mixs/estimated_size
Label estimated Size
Definition The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.
  Required: No — Repeatable: No
Examples 300000 bp
Concept Name: mixs:samp size
Normative URI http://gensc.org/ns/mixs/samp_size
Label sample size
Definition Amount or size of sample (volume, mass or area) that was collected
  Required: No — Repeatable: No

GGBN Permit Vocabulary

Index to GGBN Permit Vocabulary

By label: Collecting Permit • Contract • Copyright • Data use • Expemtion Permit • Export Permit • Genetically Modified Organism • Human Pathogens • Import Permit • Intellectual Property Rights (IPR) • Internationally Recognized Certificate of Compliance (IRCC) • Material Transfer Agreement (MTA) • Memorandum of Cooperation (MoC) • Memorandum of Understanding (MoU) • Other • Patent • Permit Status • Permit Status Qualifier • Permit Text • Permit Type • Permit URI • Permit available • Permit not available • Permit not required • Phytosanitary • Salvage • Unknown • Veterinary Certificate • permitStatus Vocabulary • permitType vocabulary

By concept name: ggbn:permitStatus • ggbn:permitStatusQualifier • ggbn:permitText • ggbn:permitType• ggbn:permitURI • ggbnvoc:Collecting Permit • ggbnvoc:Contract • ggbnvoc:Copyright • ggbnvoc:Data use • ggbnvoc:Exemption Permit • ggbnvoc:Export Permit • ggbnvoc:Genetically Modified Organism • ggbnvoc:Human Pathogens • ggbnvoc:Import Permit • ggbnvoc:Intellectual Property Rights • ggbnvoc:Internationally Recognized Certificate of Compliance • ggbnvoc:Material Transfer Agreement • ggbnvoc:Memorandum of Cooperation • ggbnvoc:Memorandum of Understanding • ggbnvoc:Other • ggbnvoc:Patent • ggbnvoc:Permit available • ggbnvoc:Permit not available • ggbnvoc:Permit not required • ggbnvoc:Phytosanitary • ggbnvoc:Salvage • ggbnvoc:Unknown • ggbnvoc:Veterinary Certificate • ggbnvoc:permitStatus vocabulary • ggbnvoc:permitType vocabulary

Concept definitions in GGBN Permit Vocabulary

Concept Name: ggbn:permitStatus
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitStatus
Label Permit Status
Definition Information about the presence, absence or other basic status of permits associated with the sample(s).
  Required: Yes — Repeatable: Yes
Examples Permit available, Permit not required, Permit not available, Unknown Material collected after 2014-10-12 cannot be in "Unknown" permit status!
Notes: Predefined vocabulary, See permitStatus vocabulary; entry of data is mandatory
Concept Name: ggbn:permitStatusQualifier
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitStatusQualifier
Label Permit Status Qualifier
Definition Description of why a certain permit was not required or why Permit Status is unknown
  Required: No — Repeatable: Yes
Examples "no national requirement for a permit at date of access", "officially authorized illegal holder", "collected on private land", "pre-Nagoya"
Concept Name: ggbn:permitText
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitText
Label Permit Text
Definition The text of a permit related to the gathering/shipping or further details
  Required: No — Repeatable: Yes
Concept Name: ggbn:permitType
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitType
Label Permit Type
Definition A permit is a document that allows someone to take an action that otherwise would not be allowed.
  Required: Yes — Repeatable: Yes
Examples Collecting Permit, Import Permit, Export Permit, Intellectual Property Rights, Copyright, Patent, Data use, Phytosanitary, Salvage, Exemption Permit, Material Transfer Agreement, Internationally Recognized Certificate of Compliance, Contract, Memorandum of Understanding, Memorandum of Cooperation, Veterinary Certificate, Human Pathogens, Genetically Modified Organism, Other
Notes: Predefined vocabulary! See permitType vocabulary
Concept Name: ggbn:permitURI
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Permit URI
Definition A reference to the permit related to the gathering or shipping event
  Required: No — Repeatable: Yes
Notes: One will eventually need a direct link to ggbn:IRCC in the future.
Concept Name: ggbnvoc:Collecting Permit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Collecting Permit
Definition A value of the ggbnvoc:permitType vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Contract
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Contract
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
ggbnvoc:Copyright
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Copyright
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Data use
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Data use
Definition A value of the ggbnvoc:permitType vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Exemption Permit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Expemtion Permit
Definition A value of the ggbnvoc:permitType vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Export Permit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Export Permit
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Genetically Modified Organism
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Genetically Modified Organism
Definition A value for the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Notes: Currently a placeholder only, might be renamed in the future
Concept Name: ggbnvoc:Human Pathogens
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Human Pathogens
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Import Permit
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Import Permit
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Intellectual Property Rights
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Intellectual Property Rights (IPR)
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Internationally Recognized Certificate of Compliance
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Internationally Recognized Certificate of Compliance (IRCC)
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Material Transfer Agreement
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Material Transfer Agreement (MTA)
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Memorandum of Cooperation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Memorandum of Cooperation (MoC)
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Memorandum of Understanding
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Memorandum of Understanding (MoU)
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Other
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Other
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Patent
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Patent
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Permit available
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Permit available
Definition A value of ggbnvoc:permitStatus_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Permit not available
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Permit not available
Definition A value for the ggbnvoc:permitStatus_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Permit not required
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Permit not required
Definition A value for the ggbnvoc:permitStatus_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:permitStatus vocabulary
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label permitStatus Vocabulary
Definition Vocabulary of ggbnvoc:permitStatus term
  Required: No — Repeatable: No
Examples Permit available, Permit not required, Permit not available, Unknown
Concept Name: ggbnvoc:permitType vocabulary
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label permitType vocabulary
Definition Vocabulary of ggbn:permitType term
  Required: No — Repeatable: Yes
Examples Collecting Permit, Import Permit, Export Permit, Intellectual Property Rights, Copyright, Patent, Data use, Phytosanitary, Salvage, Exemption Permit, Material Transfer Agreement, Internationally Recognized Certificate of Compliance, contract, Memorandum of Understanding, Memorandum of Cooperation, Veterinary Certificate, Human Pathogens, Genetically Modified Organism, Other
Concept Name: ggbnvoc:Phytosanitary
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Phytosanitary
Definition A value of the ggbnvoc:permitType vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Salvage
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Salvage
Definition A value of the ggbnvoc:permitType vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Unknown
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Unknown
Definition A value for the ggbnvoc:permitStatus_vocabulary
  Required: No — Repeatable: Yes
Concept Name: ggbnvoc:Veterinary Certificate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/permitURI
Label Veterinary Certificate
Definition A value of the ggbnvoc:permitType_vocabulary
  Required: No — Repeatable: Yes

GGBN Preparation Vocabulary

Index to GGBN Preparation Vocabulary

By label: Associated References • Preparation Date • Preparation Materials • Preparation Process • Preparation Type • Prepared By

By concept name: dwc:associatedReferences • ggbn:preparationDate • ggbn:preparationMaterials • ggbn:preparationProcess • ggbn:preparationType • ggbn:preparedBy

Concept definitions in GGBN Preparation Vocabulary

Concept Name: dwc:associatedReferences
Normative URI http://rs.tdwg.org/dwc/terms/associatedReferences
Label Associated References
Definition A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
  Required: No — Repeatable: Yes
Examples The recommended best practice is to separate the values with a vertical bar (' | '). Examples: http://www.sciencemag.org/cgi/content/abstract/322/5899/261, "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767.", "Steven R. Hoofer and Ronald A. Van Den Bussche. 2001. Phylogenetic Relationships of Plecotine Bats and Allies Based on Mitochondrial Ribosomal Sequences. Journal of Mammalogy 82(1):131-137. | Walker, Faith M., Jeffrey T. Foster, Kevin P. Drees, Carol L. Chambers. 2014. Spotted bat (Euderma maculatum) microsatellite discovery using illumina sequencing. Conservation Genetics Resources.".
Notes: Remark by GGBN: Material Transfer Agreements (MTAs)
Concept Name: ggbn:preparationDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preparationDate
Label Preparation Date
Definition The date of preparation/extraction
  Required: Yes — Repeatable: Yes
Examples 2011-01-18, unknown, not recorded
Notes: when used for tissues, quite often preparationDate is the same as | dwc:eventDate
Concept Name: ggbn:preparationMaterials
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preparationMaterials
Label Preparation Materials
Definition Materials and chemicals used in the preparation of the specimen, tissue, DNA or RNA sample
  Required: No — Repeatable: Yes
Examples for DNA: DNeasy blood and tissue kit, CTAB;
Concept Name: ggbn:preparationProcess
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preparationProcess
Label Preparation Process
Definition Process used in preparing the specimen or sample, can also be used to describe Phage/Plasmid propagation, Process used in extracting the DNA/RNA; adaptions made; SPREC code
  Required: No — Repeatable: Yes
Concept Name: ggbn:preparationType
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preparationType
Label Preparation Type
Definition Description of preparation type (specimens, tissues, DNA)
  Required: Yes — Repeatable: Yes
Examples for DNA: gDNA, eDNA, aDNA; for tissues/specimens: leaf, muscle, leg, blood
Notes: has close match to: BRISQ:Biospecimen type and BRISQ:Anatomical site

BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001)

Concept Name: ggbn:preparedBy
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preparedBy
Label Prepared By
Definition Person and/or institution responsible for or effecting the preparation/extraction
  Required: No — Repeatable: Yes
Examples Jane Doe, NMNH

GGBN Preservation Vocabulary

Index to GGBN Preservation Vocabulary

By label: Preservation Date Begin • Preservation Temperature • Preservation Type • Sequence (order)

By concept name: ggbn:preservationDateBegin • ggbn:preservationTemperature • ggbn:preservationType • ggbn:sequence

Concept definitions in GGBN Preservation Vocabulary

Concept Name: ggbn:preservationDateBegin
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preservationDateBegin
Label Preservation Date Begin
Definition Start of current Specimen, Tissue, DNA or RNA Preservation
  Required: No — Repeatable: Yes
Examples March 2012, 2014-02-19
Concept Name: ggbn:preservationTemperature
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preservationTemperature
Label Preservation Temperature
Definition Temperature of Specimen, Tissue, DNA or RNA Preservation or Storage
  Required: No — Repeatable: Yes
Examples -20°C, RT, -80°C, -196°C, LN
Notes: has exact match to: BRISQ:Storage temperature

BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001)

Concept Name: ggbn:preservationType
Normative URI http://data.ggbn.org/schemas/ggbn/terms/preservationType
Label Preservation Type
Definition Type of Specimen, Tissue, DNA or RNA Preservation or Storage
  Required: Yes — Repeatable: Yes
Examples dried, silica, alcohol, FTA card, tube, QIAsafe
Notes: has close match to: BRISQ:Type of long-term preservation and BRISQ:Constitution of preservative

BRISQ=Biospecimen Reporting for Improved Study Quality (http://www.ncbi.nlm.nih.gov/pubmed/21433001)

Concept Name: ggbn:sequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sequence
Label Sequence (order)
Definition can be used to describe sequence (order) of different preservations or other issues
  Required: No — Repeatable: Yes
Examples 1, 2, 3, 4 (1=oldest, 4=latest)

GGBN Single Read Vocabulary

Index to GGBN Single Read Vocabulary

By label: Chromatogram File URI • Fragment Length • Primer Name • Primer Reference Citation • Primer Reference Link • Primer Sequence • Sequencing Date • Sequencing Direction • Sequencing Method • Sequencing Staff • Single Sequence • Single Sequence Length

By concept name: ggbn:chromatogramFileURI • ggbn:fragmentLength • ggbn:primerName • ggbn:primerReferenceCitation • ggbn:primerReferenceLink • ggbn:primerSequence • ggbn:sequencingDate • ggbn:sequencingDirection • ggbn:sequencingMethod • ggbn:sequencingStaff • ggbn:singleSequence • ggbn:singleSequenceLength

Concept definitions in GGBN Single Read Vocabulary

Concept Name: ggbn:chromatogramFileURI
Normative URI http://data.ggbn.org/schemas/ggbn/terms/chromatogramFileURI
Label Chromatogram File URI
Definition Link to the chromatogram of an individual DNA sequence (single read)
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:fragmentLength
Normative URI http://data.ggbn.org/schemas/ggbn/terms/fragmentLength
Label Fragment Length
Definition Length of fragments (on average or precise)
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:primerName
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerName
Label Primer Name
Definition Name of primer used for this amplification, cloning, or single read
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse
Concept Name: ggbn:primerReferenceCitation
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceCitation
Label Primer Reference Citation
Definition Forst reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceCitationForward or ggbn:primerReferenceCitationReverse
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerReferenceLink
Label Primer Reference Link
Definition Link to the first reference of the primer
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerReferenceLinkForward or ggbn:primerReferenceLinkReverse
Concept Name: ggbn:primerSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/primerSequence
Label Primer Sequence
Definition DNA sequence of the primer (A,T,G,C; 5' to 3')
  Required: No — Repeatable: Yes
Notes: can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse
Concept Name: ggbn:sequencingDate
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sequencingDate
Label Sequencing Date
Definition Date when the DNA sequence/read was produced
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:sequencingDirection
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sequencingDirection
Label Sequencing Direction
Definition Direction of sequencing/read
  Required: No — Repeatable: No
Examples forward, reverse
Notes: currently to be used with ABCD only
Concept Name: ggbn:sequencingMethod
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sequencingMethod
Label Sequencing Method
Definition Method or protocol used to generate the DNA sequences/reads
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:sequencingStaff
Normative URI http://data.ggbn.org/schemas/ggbn/terms/sequencingStaff
Label Sequencing Staff
Definition Person or institution which performed the sequencing
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:singleSequence
Normative URI http://data.ggbn.org/schemas/ggbn/terms/singleSequence
Label Single Sequence
Definition Sequence of the individual DNA sequence/read (A,T,G,C; 5' to 3')
  Required: No — Repeatable: No
Notes: currently to be used with ABCD only
Concept Name: ggbn:singleSequenceLength
Normative URI http://data.ggbn.org/schemas/ggbn/terms/singleSequenceLength
Label Single Sequence Length
Definition Length of the single sequence/read (Number of base pairs )
  Required: No — Repeatable: No
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